Jonathan Christopher Morgenstern
by bonniebird
Summary: For two years Jonathan has been at war with himself. After his fathers death he learned that not all of him is evil. In fact parts of him are capable of loving small, pretty runaways who have a surprisingly tough attitude. But will Jace's meddling reawaken Jonathan's darker side.
1. Chapter 1

Jonathan Christopher Morgenstern.

Jonathan ducked through a back ally hoping to loose Luke's minions without bringing them unnecessary harm. He didn't want to enrage Sebastian and awaken his demon half but these dogs didn't understand why he was fleeing. It was for both there sakes.

"Stop this Jonathan, just destroy them." Jonathan shook Sebastian's cruel nature from his head and forced the demon's angry burning into the pit of his stomach while launching himself at a set of silver chain link fences that told him he was entering Raphael's territory. The angry yelps of a young wolf distracted Jonathan long enough for Sebastian to rise again and squirm his way to the forefront of the young Shadowhunter's mind.

"We'll kill the vampires and take their land." Sebastian's poisonous words were difficult for the boy to resist as they drawled from his own lips but a distraction from the demon appeared in the form of a small Mundane hurtling round the corner of the allway Jonathan had jumped into. The Mudane ploughed into the boy and knocking him sideways, he stumbled and fell to the floor. The Demon's laugh thundered through Jonathan's head like a nasty headache.

"I'm sorry." A small voice squeaked from above him. Jonathan looked up ready to shout at the beautifully voiced Mundane for being so useless but words failed both halves of the boy as they took in the vision before them.

The girl had a pail heart shaped face with large warm hazel eyes with flecks of shimmering gold scattered thorough them, her dark hair fell in gentle waves around her face as she looked down at the boy. Jonathan swallowed as his eyes wondered over the rest of her perfectly shaped body. She was clothed in tattered rags which had obviously once been a simple t-shirt and jeans. A dark hoodie clung tightly to her body and the sleeves were a good inch or two shorter than they should be. She smiled at him kindly and held out her hand to help him up, her actions awakening Sebastian's malicious mind.

"Oh Jonathan don't you just have the urge to devour her, she's so…. Innocent." The fair haired boy shook his head and gratefully accepted the girl's hand. Once he was up right he realised he was a good foot taller than the Mundane. Jonathan stood staring at the girl, her eyes widened as he stepped into the street light that lit the alleyway. The girl flushed and squirmed under the intensity of the boys gaze and looked over her shoulder as a crash and voice split the couple's silent moment.

"What's your name?" Jonathan asked gently,

"Amyelia, what's yours?" She asked shakily as shadows fell upon the Ally way entrance.

"Se- Jonathan." She nodded and turned to run but found her way blocked by the six foot Silver fence. Jonathan grabbed her arm not wanting a Mundane's death to be caused just because she smelt of him; he didn't put much faith in the intelligence of werewolves.

"Who are you running from?" He asked with such urgency that the girl hesitated and stopped trying to escape from his iron grip.

"My Father's monsters." She said almost in tears as three large hooded men rounded the final corner of the ally way and pulled out glinting knifes.

"Me to." Jonathan muttered before dropping her arm and allowing Sebastian to take over his body.

Jonathan awoke in a pile of bloody bodies and what he knew was his own vomit, ever since his father died he'd become conscious of what he was doing and gradually he was able to gain control over Sebastian. He wanted to change and prove to his mother that he needed her help to change. To be the son she could love. But Luke had destroyed every chance he had at getting close to her.

"Jonathan?" A small voice stopped the silent flow of tears falling from Jonathan's cheeks. He waited for his skin to heal before looking up at the gentle face of Amyelia. She handed him a plastic cup of water and a paper towel. Jonathan looked at the drink with a quizzical expression.

"The bank gives out free drinks." She muttered awkwardly when the boy didn't take the cup from her. She hadn't run from him. He'd killed these men and she came back for him. Sebastian was weak from his sudden loss of control but Jonathan knew it wouldn't be long before he was back. He decided to act quickly before his actions could be tainted by the demon.

"Do you need somewhere to stay… would you like to stay with me it'd be safer than being out here?" He stood and took the cup from the girl who seemed happy that he was able to stand on his own. She shook her head leaving an angry feeling of rejection stirring in the pit of his stomach.

"I can't you already saved me and where ever I go they find me again." She sighed and turned away from the bodies, Jonathan flinched realising she probably wasn't used to death.

"Please you look like you need help and I have somewhere to live, it's hidden… I'm sort of running to." He looked hopefully at Amyelia's back and couldn't help admire the way her hair tumbled down the sides of her hoodie and fell gently around her elbows.

"I don't know Jonathan…" She stepped away from him, Sebastian forced Jonathan's body to angrily turn the girl to face him, she gasped as she took in his twisted grimace which slowly melted into Jonathan's kind but gentle smile.

"I'm sorry… that happens sometimes, your right I'll leave." Jonathan mumbled before handing her his half drunk water and hurried away from her. Sebastian roared in protest demanding the boy to take the girl or kill her so no one else could look on such a pretty face. It wasn't until her footsteps alerted him she was following him that the demon was for once silence.

"It's ok, my dad used to get pretty mad at my mum, at least you don't lose it, much." She muttered as she glanced back at the bodies and hurried to catch up with Jonathan who was now hurrying at a tremendous speed through the back alleys of Brooklyn.

"Well here it is." The boy said hopelessly, wondering if Amyelia would just turn around and leave but to his surprise and Sebastian's glee she smiled brightly.

"It's lovely; I mean it needs some light and a bit of a clean but…" She blushed and looked up at Jonathan who was watching her clean up his dinner plate from last night he shrugged unsure of why she found the run down loft nice.

Jonathan had found a small one bed apartment in Brooklyn that wasn't on anyone's territory and the fact that Raphael's hoard of bloodsuckers lay between him and the Luke's pack was a bonus. He had spent week's learning how to hide himself from Magnus and other beings so that once he was in the building he was basically non excitant.

"There's only one bedroom, it's through there… you can have it." The boy led Amyelia through the dark dusty living room to a large white room that was lit by on small skylight. The room was empty apart from a large double bed with an old looking metal bed frame and a picture of a slender woman with shocking green eyes taped to the wall. Jonathan looked at the picture lovingly before smiling to Amyelia and ducking out of the room in a polite manner.

"Wait I can't take this room, it's the only one with a bed I'll sleep on the sofa." A dark smile played over Jonathan's lips and for a second his black eyes seemed to swallow Amyelia but after a few moments he was back to normal and simply refused to put a lady to sleep on anything but a well-made bed. Amyelia had never been called a lady before and agreed with him hoping he'd leave before he saw her blushing.

"I'll leave you to sleep." Was all he said before shutting the door and leaving her alone.

"Oh Jonathan, aren't you tempted to sneak in while she's asleep, touch her skin… take her soul." Sebastian tried to pull Jonathan back towards the room where Amyelia was sleeping but Jonathan refused and instead hurried into a study which was hidden by a numerous amount of wards.

Once Jonathan had settled he had started looking for ways to get rid of Sebastian, trying desperately to look for a way to rid himself of demon blood and return to his family, it had taken him two years to come to the decision but once it had wormed its way into his head it stayed much to Sebastian's anger.

"Leave her alone." Jonathan hissed as he looked in the mirror he had hung in the centre of his study. The walls were covered in paper and manuscripts of how to rid demons but nothing helped him, not even the seelie queen would offer him a deal.

"Why, she won't love you Jonathan… is that what you want someone to love poor evil Jonathan." Sebastian grinned devilishly at Jonathan in the mirror. The Shadowhunter removed his black jacket reviling his toned arms that were covered in runes.

"Because I told you to, I'm just helping her." Jonathan glared at the mirror but Sebastian tilted his head to the left as Jonathan tilted his head to the right knowing it would annoy the Shadowhunter and distract him from the papers he was looking over.

"No, you wish you could kiss those soft rosy lips of hers, her body's just the right size for you to cradle to your chest while she sleeps. I'm in your head Jonathan, you can't hide from me." Sebastian chuckled darkly when a wave of anger washed over the shadow hunter as the demon's taunts struck a nerve.

"SHUT UP!" Jonathan yelled at Sebastian before pulling his stele from his boot and drawing a sleeping rune on his arm and heading into the dirty living room. He flopped down on the sofa as the rune knocked him out and happily slipped into the dark comfort of sleep.

Amyelia woke up for once feeling well rested, the sunlight streaming into the bedroom making Amyelia feel warm and lazy despite the many hours of sleep she'd had. Deciding to get up Amyelia stretched, her arm hit against something soft and knocked it to the floor with a quiet thud. She quickly hurried to retrieve what she now realised was a simple white cotton dress a black hair ribbon and a matching pair of black ballet flats with ribbons on. A note was tucked neatly in on of the shoes in a delicate scrawl.

Amyelia, I've gone out so don't go outside or answer the doors unless you're sure I'm there

Jonathan.

Amyelia shrugged and got dressed happy to finally be out of her old clothes and decided to explore the loft.

Amyelia discovered that the door she had originally thought was a closet was a tiny bathroom with one small window which was covered in paper so that only a tiny sliver of coppery light shone into the room. She pulled on the paper and allowing the room to be flooded with light Amyelia blinked in the sudden brightness and tutted at the state of the bathroom. It was neat and tidy to a point, it needed a through clean but nothing a god hour or two couldn't fix. Amyelia's mother used to carry her around while cleaning and although to most would find house work a menial task Amyelia loved it, it was the one thing that reminded her of her mother. To her delight there were some old bottles of cleaning product the cabinet beneath the sink.

Amyelia set to work on the bathroom and was satisfied with her quick work. Once she was sure the bathroom was clean she skipped into the lounge carrying a bucket of cleaning product. The dark room was dusty and covered in sheets. The first thing Amyelia did was pulling all of the large sheets down from the windows and rolled them all into balls. She cleaned for what must have been hours because when she was done she collapsed on the sofa and drifted to sleep.


	2. Chapter 2

Amyelia was jerked awake by a horrible grinding noise, a panic rose in her stomach as the lock on the front door began to shake violently and hushed voices filled the air. Unsure of what to do Amyelia rose to her feet and waited. As soon as the door handle dropped to the floor Amyelia ran from the room and into the bedroom. Several footsteps echoed through the loft, Amyelia crawled onto her stomach and slide herself under the bed. There was barely enough room for her to breath, just as she was out of sight the bedroom door burst open and four feet clad in black leather boots walked across the floor stopping mere inches from Amyelia's face. She covered her mouth to stop a terrified scream slipping past her lips.

"Alec you said we'd find him here." The set of feet to the left of the room stomped towards the door closely followed by the second pair. Amyelia let out a quiet sigh of relief as the door started to shut.

"Wait Jace." The second pair of feet returned and Amyelia closed her eyes praying silently that they wouldn't find her the sound of metal scarping against wood forced Amyelia to jerk her eyes open. A pair of piercing blue eyes framed by dark black hair were gazing at her, a second set of blue eyes joined them. No one moved and Amyelia swore she could feel the seconds pass by.

"Who are you?" The dark haired boy asked. Amyelia whimpered and attempted to shuffle away from the boys but found she had nowhere to go. Panic washed over Amyelia as the dark haired boy attempted to reach for her. The second boy vanished causing Amyelia to divert her attention from the boys grabbing hands and follow the footsteps of the other boy who was now stood next to her. The bed slid across the room Amyelia attempted to shuffle along with it but was grabbed by the second boy just before she could escape his grasp.

"Get off me!" Amyelia screamed trying desperately to get the boy to let go but no matter which way she twisted his grasp on her didn't loosen. The black haired boy crossed the room in a few steps a silvery blade glinting in his hand, Amyelia snapped her eyes shut refusing to take in the scene before her. She was stupid enough to trust another human being with her life. A surprised cry filled the air and the next thing Amyelia knew she was flung hard against the wall as the boy who was holding her was ripped away from her.

Jonathan had arrived and he looked furious.

He threw the blond haired boy out of the room and held a blade menacingly towards him.

"GET OUT WAYLAND." The boy was about to dive for Jonathan but the dark haired boy pulled him out of the building, as soon as he was sure the pair had gone Jonathan hurried over to where Amyelia was cowering and dropped to his knees.

"I'm sorry." He whispered he went to pull Amyelia into a hug but hesitated.

"What happened?" Amyelia asked wincing as she tried to stand up but was forced back down by Jonathan's strong hands pulling at her arms. He pulled of his jacket and balled it up placing it against Amyelia's head. Amyelia gasped as she took in intricate tattoos that were visible through his white t-shirt, she blushed when she saw the satisfied smirk on Jonathan's face.

"Jace Wayland… he's not to be trusted, I thought we were safe here." Ameyelia didn't press the matter any further for two reasons, one Jonathan looked so angry Amyelia began to wonder if he'd have another outburst like he had in the alleyway the day before and two Jonathan's face was very close to hers and she was starting to notice just how incredibly handsome the fair-haired boy was.

"Jonathans' holding a girl captive." Jace declared as he entered the old police station where Magnus, Luke and the rest of his pack were waiting for the two Shadowhunter's to return.

"You know he's holding her captive or you assume he's holding her captive." Luke asked sternly as he rubbed the top of his nose with his fingers.

"She hid from us, he's probably told her were dangerous." Jace snapped back, Luke was getting worried by how continuously Jonathan attempted to get to Jocelyn and how successful he was last time. He'd managed to get a letter to her filled with drawings and runes that had Luke stumped but the silent brothers were convinced they were runes that forced Demon's from Mundane bodies. She was now convinced that Sebastian needed her help. Jace however just wanted to kill the boy and Luke couldn't really blame him.

"That's not enough evidence to ask the Clave for backup in retrieving them from the residence Jace you know this." Luke sighed.

"She's clearly malnourished and In need of a bath… she was locked in the building, if we hadn't known the loft was there we wouldn't have found her until she left." Alec mumbled quietly, his paribati smiled thankfully at him. Luke had to give the pair their dues they were still hurting over the loss of Max, Robert had left Maryse after Izzy had been badly injured during a patrol. If it wasn't for Clary's runes she would have died.

"That's better, boy's you need to wait until I get orders from the clave to bring him in, he's sick… I know what he did, it hurt us all but you need to be rational about this." Luke fixed Jace with a hard stare before hurrying off with Magnus informing him of what he was planning to do.

"Jonathan, it's stopped bleeding, I'm ok really." Amyelia smiled gently at Jonathan who was fussing over the wound she'd received after being rammed into the wall.

"I didn't mean for you to get hurt…" He rubbed the back of his neck awkwardly and sank back into the sofa making Amyelia bounce on the uneven springs, a silver chain caught her eye and before she could stop herself she pulled on it. A small wooden toy soldier in a tiny glass jar was suspended from the chain. Jonathan pulled it off and let Amyelia inspect the detailed toy soldier. He watched her carefully ignoring the images Sebastian showed him.

"It belonged to… a friend." His voice rumbled darkly a sign Amyelia had come to realise in her short time with Jonathan that meant she was pushing her luck. She smiled and quickly dropped the toy into his open palm.

"It's very beautiful." She muttered, Jonathan was still for what seemed like hours but was only a few seconds before leaning over and placing the toy around her neck.

"I use it as a reminder; I won't be like my father… I will never hurt people I love like he did, not again." His eyes lingered on the toy and Amyelia could see something dark flickering inside Jonathan's black eyes. She reacted without thinking and leaned across the sofa, pressing her lips to his. She wasn't sure what to do next as she'd never kissed someone before and Jonathan seemed to freeze and stiffen complete which made her panic a little.

As she began to pull away one of his hands tangled into her hair pulling her face back to his, his lips brushed against hers waiting for her to respond to him, her body obeyed without her control as his other hand wrapped itself around her waist and pulled her against him. He pulled away suddenly and stood up still Holding Amyelia tightly to his well-toned chest.

"Stay close to me." He commanded with such authority that his body seamed to vibrate. Amyelia nodded as he pushed her behind him. The front door burst of its hinges as Jonathan pulled two short blades that began to glow when he muttered something to them. Amyelia clutched tightly to Jonathan as the Jace boy stepped into the room closely followed by the woman from the photo in Jonathan's bedroom. Within seconds Amyelia could see the resemblance's between the woman and her rescuer. He looked just like her, but his eyes were black, she was wearing a simple green dress that stopped below her knees, her neck was covered in licks of black markings like Jonathan's.

"Jonathan, please calm down… give me the girl." She smiled gently and held a hand out expectantly. Jonathan took a step back and tucked an arm around Amyelia shielding her from the intruders view.

"NO, why are you here." He snapped trying to herd Amyelia towards the door which was now unguarded.

"You're sick Jonathan, the silent brothers read your papers and Luke's at the Halls now… Maryse, she doesn't forgive you but she understands that you weren't acting as yourself…please son let me help you." The woman began to cry as Jonathan backed away from her advancing steps.

"He doesn't touch her." Jonathan said dangerously pointing a blade at Jace who was leaning lazily against the wall.

"She goes back to her family." Jace snapped slowly. Amyelia clutched at Jonathan who twitched as if trying to stop himself from moving.

"No, she stays with me." Jonathan said forcefully, the lady indicated for Jace to leave who did after hesitating and muttering he'd be outside the door and sat down on the sofa causing Jonathan to back up across the room away from her.

"Jonathan, may I talk to the girl, please." She asked kindly, the warmth in her smile was the same Amyelia felt while under the gaze of Jonathan. The boy hesitated and glanced at Amyelia who was staring in fascination at the lady.

"If she wants to talk to you." Jonathan's reply caught the woman by surprise, she watched with wide eyed fascination as Jonathan turned to face Amyelia.

"Don't leave." She squeaked, Jonathan nodded and pushed Amyelia in front of him but wrapped an arm around her waist possessively.

The green eyed woman took this as a good sign and smiled at the girl hoping she would relax.

"What's your name darling?" Amyelia was surprised by the simple question.

"Amyelia… but Jonathan calls me Amy" The green eyed woman smiled in delight.

"I'm Jocelyn and I'm the resident Shadowhunter of Brooklyn, were taking Jonathan to the New York Institute… has he told you anything about us?" Amyelia frowned and shook her head, Jocelyn nodded and carried on.

"Right, well then why are you here?" Jocelyn asked bluntly.

"Father sent hunters after me; Jonathan saved me and let me stay here." Jocelyn's eyes grew wide.

"Your father… he works for Raphael?" Amyelia nodded.

"He's sort of my uncle I guess, but he doesn't believe I should be under my father's care." Amyelia nodded. Jocelyn turned to Jonathan and smiled.

"She is the vampire, Nephlim hybrid that your father spoke of… I didn't believe her birth was any more than a myth but we can take her with us if she would like to be trained… but if she wants to leave you need to let her." He face turned stern and Jonathan's arm tightened around Amyelia's waist.

"I'll come with you, its ok." Amyelia whispered to him relived that he'd relaxed at her words. Jonathan dropped his head onto Amyelia's neck and watched Jocelyn leave; the pair could hear her talking to Jace. Once she was out of sight Jonathan tilted Amyelia's face to his and let his lips brush against hers.

"I wouldn't let you go any way Amy." She tensed as Jonathan's dark eyes flashed dangerously.


	3. Chapter 3

Amyelia's eyes widened as she took in the giant hallways in front of her, she turned to a red headed girl Jonathan had greeted as Clary.

"You live here?" She whispered to the girl who chuckled before shaking her head and leading her up the flight of stairs.

"No, I live in Brooklyn with mum and Luke, he's a werewolf, Jace and Alec live here with their mum and sister Izzy… she's dating my friend Simon." Clary chattered absent minded. She smiled kindly at the brunette and stopped in front of a room and indicated for her to go inside.

Amyelia gasped when she stepped through the door. The room was huge; a gold and pink double bed took up one wall while a vanity desk with a large gold framed mirror stood proudly between two white doors that had a gold trim. Clary dragged the awe struck girl over to the first door and proudly showed her a large bathroom which was in the same gold and white with fluffy pink towels and soaps.

Finally Clary led Amyelia to the last room which turned out to be a huge walk in wardrobe. A tall dark haired girl wearing a black peplum top and a pair of tight black skinny jeans burst in the room.

"Clary have you seen my new stil… oh hi cutie." Amyelia blushed as the girl looked her up and down before turning back to Clary who had hurried out of the room returning a few minutes later with a pair of stiletto boots.

"Izzy this is Amyelia, she's the girl that was with Saba… Jonathan." Clary muttered awkwardly as she handed the tall girl the shoes and smiled at Amyelia, the three stood awkwardly until Izzy squealed girlishly making Amyelia jump.

"You have hardly any clothes, Clary you know what this means…" Izzy was now jumping up and down causing Clary to laugh at her.

"Let me guess, were getting Magnus to zap up some shops for us?" Both girls squealed happily again while Amyelia stood wide eyed.

"Is this my room?" she asked quietly finally finding her voice, Clary nodded before ushering Amyelia out of her closet and back towards the corridor.

"That was Izzy, I'll take you to meet her brother Alec, he was there when Jace found you." Clary lead Amyelia through the Institute naming of rooms as they went past them. Eventually Clary stopped in front of a room at the end of a corridor, two heavy oak doors covered in carvings of weapons. Clary knocked before ushering Ameylia inside.

"This is out training room; the boys are all ways in here." Clary sighed, Jace dropped down from the celling landing neatly next to Clary who rolled her eyes before allowing him to kiss her gently. Alec appeared next to the couple and rolled his eyes before holding a hand out to Amyelia who shuffled closer to Clary. She was comfortable with Clary, she had sat with Amyelia while the adults had inspected Jonathan. Maryse insisted that Clary take Amyelia upstairs before they settled Jonathan in. Alec gave her an odd look before shoving his hand in his pocket.

"Where's Jonathan?" Amyelia asked Clary who hurriedly glanced at Jace.

"Around." He shrugged before pulling Clary into a tight hug. Amyelia frowned but didn't ask any more sensing that the group didn't want her to see Jonathan yet.

"Dinners ready." Izzy's voice boomed through the hallways, Clary poked her head round Amyelia's door before she could put her book down.

"I'd stay in there, Izzy means well but she's not the best cook." Clary winked at her before vanishing. Amyelia sighed and got up deciding to make her own mind about Izzy's cooking.

When she eventually found the kitchen she was surprised to see a familiar face.

"Simon." Amyelia gasped happily as he pulled her into a tight hug.

"I see you managed to escape again, your dad not found you this time I assume." Her old friend chuckled.

"No… well they did but Jonathan saved me." Amyelia babbled on explaining how she arrived at the Institute. Simon chuckled and accepted a plate of spaghetti bolognaise from Izzy who looked utterly confused.

"How do you no Simon but not Clary or her mom?" The Shadowhunter asked rudely.

"My Uncle Raphael sent for Simon to watch over me while your people summoned him some where… my mother had the same mark that Jace has on his wrist on her left shoulder. My uncle Raphael turned her, my father used to love her and he begged Uncle Raphael to save her… Simon stoped father from killing me but he couldn't save my mother." Izzy put a hand gently on Amyelia's shoulder as tears fell down her cheek.

"So your mother was a vampire who used to be a Shadowhunter, the Clave will probably want you on the council as a representative or something stupid like that." Izzy sighed before dishing some food out for herself.

"I don't think the vampires would like that, um Izzy… how much garlic did you put in this?" Amyelia asked as she and Simon downed there water trying to was away the taste.

"Oh god it's awful isn't it so much for my cooking lessons." She sighed before taking the plates of food of the pair and grabbing some microwave meals from the huge fridge that stood in the corner of the room.

"It was ok, you just need to follow a recipe." Amyelia muttered bravely, Simon gawked at her. No one said anything like that to Izzy. Not even Alec and Maryse.

"Oh really." Izzy turned to face the smaller girl with her hands on her hips, Amyelia glance nervously at Simon before shrugging. She might as well go the full mile.

"Yes, you have the right ingredients just not the right balance of them… less garlic, more tomatoes and a bit of salt in the pasta water and it would have been fine." Amyelia swallowed as a furious looking Izzy stared down at her.

"You think so?" Izzy's stern glare turned soft as she mulled over what she had said. Amyelia nodded before scoffing down the microwave cottage pie Izzy set down in front of her.

Once she was finished she thanked Izzy, hugged Simon and ran down to the meeting room to see if she could find Jonathan. To her dismay she collided with the leather clad chest of Jace before she could reach the huge double doors of the meeting room.

"You're not supposed to be down here." He snapped coldly, Amyelia flinched at his bellowing voice and tried to dodge past him but he gripped her arm and marched her back up her room. Izzy started yelling at Jace for manhandling Mundane's but he ignored her and shoved Amyelia roughly into her room before vanishing down the now dark corridor.

Amyelia sat for hours curled up in the centre of her bed, she couldn't sleep. A light tap on her door alerted her of someone's presence.

"Jonathan?" She whispered hopefuly, Izzy's musical chuckle sent Amyelia's heart plummeting into her stomach. The beautiful Shadowhunter hurried into the room and sat on the bed next to the plain looking girl.

"You know if you can't sleep a dungeon is a good place to look around and get rid of your curiosity." Izzy winked before pulling on a black shiny jacket with silver buttons up the front.

"Where are you going?" Amyelia asked quietly before hesitantly allowing Izzy to pull her of the bed and onto her feet.

"Simon's, now come on." Izzy hissed under her breath as the pair quietly snuck down stairs, the only noise Amyelia could here was her own breath and the quiet clacking of Izzy's heels on the marble floor. Once they reached the front door Izzy gave Amyelia directions to the dungeons before heaving open the door and slipping outside.

Amyelia hurried down a corridor to her right and took the second left like Izzy had told her. Her heart skipped happily as she found the door Izzy had told her lead to the dungeon. With a sharp tug the door opened wide enough for her to squeeze through.

Amyelia couldn't help but notice how cold it was down here, a loud clank had her heart pounding so loudly she was sure everyone in the building could hear it.

"Jonathan… it's me Amyelia." She whispered shyly, a low moan echoed around the room and Amyelia's slow shuffle broke into a run when Jonathan muttered a painful reply. Once she found the room he was locked in she slid the bolts across on the door not caring about the loud slamming noise they made. She happily flung herself around Jonathan who scooped her into his arms despite what looked like a nasty gash down one of his arms. Amyelia moved the glowing rock, that had been shoved carelessly onto a shelf above Jonathan's head, so she could get a better look at him. A horrified gasp slipped past her lips as she took in the sight before her.

Jonathan's shirt was torn and stained red, fading cuts covered his chest and arms but Amyelia's eyes stayed on Jonathan's face. His face had been burnt and melted by his tears.

"Jonathan you said they would help you." Amyelia whispered as she swallowed the lump that had lodged itself in her throat. He shrugged and pulled her against his chest and rested his head on hers.

"I heard Jace yelling at you earlier." He muttered. Amyelia tried to reply but was too distracted by his fingertips that were tracing odd shaped across her back and only managed an odd squeak causing Jonathan to chuckle.

He hummed gently to her until she fell asleep. The young Shadowhunter fought of his own exhaustion knowing to well that Sebastian would have control as soon as he was asleep.

Jonathan wanted her to feel safe in the Institute, He wanted her to have friends and get on with his family. But Sebastian didn't.

Both halves of the boy sat in silence each mulling over the day's events, planning there next moves carefully. Jonathan tried desperately to entice the demon by allowing alluring thoughts filter through his mind. But by morning the boy was only certain of one thing

The Demon wanted her.


	4. Chapter 4

JCM chapter4

"Amy, hey wake up." I woke up to Jonathan's lip gently brushing against neck; I gasped as his teeth grazed my skin causing a deep chuckle to rumble through his chest a dark glint flickered through Jonathan's eyes.

"Sebastian." I muttered disappointedly and turned away. The Demon gripped my chin a little too tight and moved my face so I couldn't look away from him.

"How did you know sweetheart?" Sebastian drawled before kissing me fully on the lips. He started choking loudly as soon as our lips connected, Jocelyn was suddenly running down the dungeon corridor she skidded to a halt and looked down at us. Sebastian managed to cough out a growl as Jocelyn tried to help me get away from him.

"I don't know what's happening he was fine until I kissed him." I stuttered at her, I was surprised to see a small smile spread across her lips. Sebastian yanked me across the dungeon away from the slender woman and forced me against his chest.

"Mine." He hissed, Jocelyn stepped back and looked directly at me. Sebastian span around so that I could only just see over his shoulder two dark shapes moved behind Sebastian and the next thing I knew Jace with the help of Luke had lifted Sebastian of his feet and Alec was trying to pry me from his grip. After a few minutes of struggling I fell into Jocelyn who steadied me before calling Clary who rushed me out of the dungeon and up to my room as I left caught a glimpse of Sebastian pushing of Luke and hitting out at Alec who only just ducked in time.

"What happened to him?" Amyelia asked quietly as Clary sat her down at her dresser, Izzy wondered in a few minutes later a large scratch on her cheek was fading. Clary began brushing Amyelia's hair and tied it into a ponytail with a thick plait running through it Clary glanced awkwardly at Izzy who shook her head. I sighed and tugged gently at the chain around my neck and rolled the glass case that held Sebastian's little toy soldier. Both girls gasped at the same time and when I looked up their reflections wore matching expressions of surprise, Tears began to trickle down Izzy's face as she stared at the little glass jar between my fingers.

"Where did you get that?" Clary asked harshly, I tucked the glass jar into my jumper and shiffeted uncomfortably under the girls' gaze.

"Jonathan gave it to me; he said he wore it to remind himself to not be like his father." I muttered quietly hopping Clary, who looked so angry that she was shaking, would calm down.

"So Joceys right… they are two people he's not all Sebastian." Izzy said her voice cracked as she slumped down onto my bed, I frowned and turned to Clary who hurried over to Izzy and pulled her into a tight hug.

"You're his sister how can you not tell the difference between Jonathan and Sebastian, I've known him for a week and I can tell." I had to grip the edges of the stool I was sat on to stop myself from crossing the room and furiously shaking the red head. Clary fixed me with a disgusted look and was about to shout at my when Izzy stood up.

"Because when his father alive there was no Jonathan, he was all Sebastian… Sebastian killed my little brother Max and that toy you're wearing used to be his." She didn't yell or sob she just spoke calmly as if she was detached from the topic. I placed my hand over the little soldier and felt a twist in my stomach as I processed what Izzy had said.

"Our father experimented on us when we were younger, Jonathan was feed demon blood he was born Sebastian… Mum loves him as much as she loves me but until she knew she could save him she couldn't bare look at him, she felt like she had failed him." Clary muttered quietly.

"Your father… experimented on him?" I whispered, Clary exchanged a look with Izzy who nodded and said she needed to talk to her mother leaving the two of us alone.

"I'll tell you what happened… just please don't judge my mother to harshly she was trying to keep me safe… I just couldn't see it back then." She whispered the last part; I nodded and crossed my legs as she explained what happened over the last few years.

Jonathan hated it when Sebastian was in control, he could see and hear everything that the demon was say but could do nothing about it. He tried to force himself to gain control but the cruel creatures rumbling laugh made the boy flinch, or it would have done if he could move his own body. If he didn't fight he could see everything that was happing around him but when he fought Sebastian the monster pulled them into a horrifying world of shadows, he couldn't see anything around him but he could hear screams just when Jonathan felt his strength waning and his vision slowly started to return as Sebastian slipped into full control. A blurred shape that made a loud clacking noise when it moved hurried across his eye line.

"Girls what did it tell you about bringing her in here."

"Mum, Mum… we can help him he's not putting it on look, Amy come here show Mum."

Jonathan saw her… it was definitely Amy the only thing in the room that wasn't a blurred was her and she was far too pure to be a product of Sebastian's. She was holding a silver chain in her hand there was a hushed gasp from everyone in the room. The blurred group gathered around her and Jonathan began to panic.

"Amy." He gasped desperately suddenly he found a new strength and closed his eyes forcing himself into his own darkness.

"She so pretty isn't she, I wonder what he blood smells like." Sebastian drawled.

"I wonder how long it will take her to get rid of you." Jonathan spat back he could feel people around him, he could hear his mother calling his name begging him to come to.

"Go on Jonathan wake up and we can have some fun." Sebastian forced Jonathan's mind to see himself coated in a thick layer of blood his blond hair was now a dark red , he slicked it back as thick rivulets of blood dripped onto his shoulders. He was crouched among the dead bodies of his mother and the Lightwoods clutched to his blood soaked body was Amy. Jonathan took a breath and forced himself to imagine a body of his own making the Jonathan in front of him smile darkly.

"Amy?" Jonathan whispered as he hesitantly stepped forwards. He stopped and gaged when he saw what Amy was doing. At first he thought her head had been buried into his shoulder but now he could see her lapping blood from the creature that was holding her, her two small fangs grazed it's neck making it moan deeply. Jonathan felt anger run through his body and launched himself at the pair in front of him he gasped as a sharp pain burst through his head.

"I'm in control now." Jonathan looked up at the blood soaked version of himself its green eyes darkened until they were black. Jonathan smirked up at Sebastian and took a deep breath as he realised he could play Sebastian at his own game.

"Dumb move bub." He chuckled darkly and pictured himself in the main meeting room where he was being cured. His eyes snapped open and the demon cried out in shock as Jonathan for the first in his life completely silenced the monster within him without the help of runes. He was gasping for air slowly he looked up at Jace who was stood by his side blade in hand his face was twisted with concern and a cold calculating grimace.

"I did it." Jonathan gasped as a grin settled over his face; Jace gave him a surprised look and indicated of Maryse to come over.

"Jonathan?" She asked carefully, the boy nodded and grinned as he wiggled in his restraints testing his new freedom from the darkness.

"Yeah I'm Jonathan." He whispered to himself making Jace snort, Maryse shot him a nasty look and the blond boy quickly fell silent.

"You don't feel him with you." She asked slowly Jonathan shook his head and looked up at her and she gasped.

"What?" Jonathan asked suddenly panicked Jace frowned and looked down at him he frowned and gripped Jonathan's face forcing him to look directly at him.

"His eyes are green, aren't they normally black?" He asked Maryse who nodded and hurried out of the room saying she would bring a silent brother to talk to Jonathan about what he did.

"Why Jace if I knew you liked looking into my eyes I would have spent more time gazing at you like my sister does." Jonathan snorted, with a sly smirk. Jace chuckled before realising who he was joking around with and hurried out of the room after his mother.


	5. Chapter 5

JCM Chapter 5

"Bring your hand up to your chin and don't tuck your thumbs, that's how you break them." Jonathan laughed as Amy tried to throw a punch but missed, he grabbed her wrist and span her into his chest and with one swift movement had both her hands behind her held tightly in one hand and her wooden training blade in the other hand.

"This so isn't fair Jonathan." Amy pouted a tried to knock Jonathan of his feet by swinging her legs at his ankles, he flipped her over his shoulder before she could make contact with his legs and dropped her with a gentle thud on the floor.

"Why, cause you can't win?" He grinned; he was kneeling over her holding himself up on his elbows, the closeness made Amy blush. She placed her arms flat on his well-toned chest and tried to push him of her, hoping to get some leverage in their fight but found it only made her arms tired.

It had been three weeks since Jonathan had overcome Sebastian and the demon hadn't resurfaced although everyone but Amy and Jonathan were on tender hooks waiting for Jonathan to explode. Jonathan had started training Amy as soon as the Silent Brothers confirmed he was cured and loved the fact that she could easily disarm Alec within minutes of practising with him.

"No, cause your better than me." She grunted as she swung for his face again however this time she made light contact with the side of his cheek. He stood still stunned that she had managed to hit her target as hand to hand contact was one of her weakest areas of expertise. She had taken too sword play and throwing steels as if she had been training as long as the rest of them and managed to beat everyone but Jace although Jonathan was pretty sure Izzy had let her win after Jace's ungracious victory dance.

Jonathan's pov

I ducked as she swung a leg to catch me in the gut but grabbed her foot and was about to pull her off her feet when she used my grip as leverage and pushed herself into the air and wrapping her legs around the back of my neck. I grunted as her sudden weight dislodged me and we went crashing to the floor.

"Not bad." I grinned as I rolled over and flipped myself onto my feet while pulling her up, she grinned and skipped out of the training room telling me that she'd be with Izzy and Simon in the meeting room. I started to gather the weapons we had been using when a loud high pitched screeching burst through my head making me drop the weapons and clutch at my head as my vision blurred. I began to gag and scream as my skin felt like it was on fire from the inside out, I hurtled out of the room desperately trying to make sense of the direction I was going in as the pain blurred my vision and slowed my movements.

Then just as suddenly as it started the pain stopped and I realised I was staring at myself in one of the huge mirrors that decorated the halls of the institute. For a second my eyes flickered black and my reflection grinned at me.

"Did you really think that would work Shadowhunter?" Sebastian's voice echoed harshly through my head. I swallowed and closed my eyes trying to figure out if it was my imagination or whether the demon had in fact returned. I didn't feel any different so I shrugged it off and returned to the training room trying to occupy my mind.


	6. Chapter 6

Amyelia's POV

My eyes snapped open as the huge bed I still wasn't used to dipped and familiar arms wrapped themselves around me, Jonathan's lips pressed gently to my neck I slumped against his chest and began falling asleep again it wasn't until his teeth sank into my neck a little too harshly that I flinched away from him realising something was wrong.

Jonathan had been sneaking into my room and curling up with me each night since he had gotten better but he had never been so brash. When I rolled over to face him my eyes met cold black ones.

"Sebastian." I sighed trying to shuffle away from the strong arms that kept me pinned to the demon's chest. He chuckled darkly when I tried to pull away from him but he quickly stopped when he began coughing and chocking he turned away from me and when he looked back his eyes were a vibrant green. I sighed with relief as Jonathan regained control over his body and pulled away from me slightly shifting so that we weren't so close.

"When did he come back?" I whispered to him, he didn't look at me a tell-tell sign he didn't want to tell me. As much as I enjoyed Jonathan's loyalty and never-ending protection his choice to exclude me from the part of his life that involved Sebastian was starting to take its toll.

Jonathan was struggling to keep Sabastian's return a secret, he wasn't sure how his family would react to the demon coming back. They had started to accept him, his mother would smile at him and even Jace would ask Jonathan for hints or ways to improve his fighting.

He'd been enjoying going on patrols with the Lightwoods who had taken Max's soldier and had it enchanted by Magnus so that nothing could damage it. They gave it back to him the next day along with the promise that they truly forgave him for Sabastian's actions.

The thought alone had made him weak at the knees, that after all the pain he'd caused. They were still willing to help him. He looked up from his seat on the high window as Amy walked into the library looking for him. She gazed past him and out at the city below as she took a seat next to him.

"Your mother found… something Sabastian left for her." She whispered, crossing her arms and leaning them on his knee so she could prop her head up and look aver him in his reclined position.

"I heard." He pointed to the mark behind his ear, he'd told her it was a permanent hearing mark which was why, unlike his other marks, it hadn't faded into a scar.

"He wrote on the hall way walls that he won't let you escape… Maryse is having the Clave send the best medics here, she thinks that there is a small chance that there are more children like you." Amy mumbled. Jonathan parted his legs and pulled Amy up so she could rest her head under his and wrapped his arms around her, holding her close.

"Have Clary and Jace volunteered to be part of the tests the Clave will do?" He asked quietly, breaking their sleepy silence. The sunlight let a warm feeling wash over them making the moment more comforting than it should have been, considering the day's events.

"Yes, they said they'll only let the Clave have you if they take them as well which is how they gave into Maryse's demands, all three of you will be examined over a period of time." She mumbled, her breath hitched as he began drawing imaginary runes on her back. Sabastian began putting pressure at the base of his neck a warning that the demon was slowly forcing its way through his body.

He shoved her off him and began stumbling away from her, he made it to the hall way, almost colliding with Jace and Alec. His legs were the first to go, then his arms. The part of him to be taken over was his eyes, Jace had to watch as Jonathan's eyes slowly turned black, like treacle pouring into a jar of water making him feel queasy.

The screams echoed through the Institute. They weren't the screams of Jonathan's pain, but screams of frustration as again and again he had to fight off the demon who showed no sign of giving up his place in the boy's body.

"When you touch him it makes it easier to Jonathan to fight him, we had hoped that maybe a combination of vampire and Shadowhunter would be a sort of cure." Maryse explained to Amy who was sat with Izzy, going over baking ideas and tips.

"So the only way he can get better is by fighting?" she asked quietly, Izzy ran a hand over her shoulder, feeling a little sad herself as they had gotten closer over the time the demon had been absent.

"No, the runes he found are helping him but they don't last for more than a few hours, Clary and Jocelyne are working together to strengthen them." Maryse said softly, comforting the girl who smiled and nodded.

"Then while he's fighting I'll train… I'm no use moping around so I might as well learn how to help you all." Amy said firmly looking up at Izzy, who was staring at the girl with admiration.

"I'll train you up so well you'll have the angelic mark on your arm by tea time." Izzy said with a grin as she jumped down from her seat. Maryse smiled as she watched the girls walk to the stairs the lead to the training floor. She fondly recalled training alongside Jocelyne for a short time and hopped that this new girl could hold the group together because she could feel something coming for them and it was far worse than anything the cruel, childish demon could conjure up.


End file.
